RNA Velocity using scVelo¶
Marissa Esteban
Data: CITEseq YS006_UW
I did pre processing in Suerat and saved object as .h5Seurat to perform RNAvelo in Python wtih scVelo
In [1]:
# Setup
import scanpy as sc
import scvelo as scv
import anndata
import loompy
import mygene
import scipy
import seaborn as sns
import matplotlib.pyplot as plt
In [3]:
h5ad_path = "/Volumes/PortableSSD/IntegratedMultimodal_CITEseq.h5ad"
adata = sc.read_h5ad(h5ad_path)
adata.obs.index = [x.split('-')[0] for x in adata.obs.index] # TTTGGAGTCGGTTGTA-1_1
loom_paths = ["/Volumes/PortableSSD/YS001/possorted_genome_bam_KLWV0.loom",
"/Volumes/PortableSSD/YS002/possorted_genome_bam_PNEM4.loom",
"/Volumes/PortableSSD/YS003/possorted_genome_bam_8Q2XV.loom",
"/Volumes/PortableSSD/YS004/possorted_genome_bam_0XB2N.loom",
"/Volumes/PortableSSD/YS005/possorted_genome_bam_HX08G.loom",
"/Volumes/PortableSSD/YS006/possorted_genome_bam_751VB.loom"]
combined_loom_path = "/Volumes/PortableSSD/citeseq_combined.loom"
loompy.combine(loom_paths, combined_loom_path)
ldata = sc.read_loom(combined_loom_path)
ldata.obs.index = [x.split(':')[1] for x in ldata.obs.index] # possorted_genome_bam_751VB:AAAGTCCGTAAGGTCGx
ldata.obs.index = [x[:-1] for x in ldata.obs.index]
WARNING:root:â•── 'batch_scan_layers' is deprecated. Use 'scan' instead WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471 WARNING:root:â•── 'batch_scan_layers' is deprecated. Use 'scan' instead WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471 WARNING:root:â•── 'batch_scan_layers' is deprecated. Use 'scan' instead WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471 WARNING:root:â•── 'batch_scan_layers' is deprecated. Use 'scan' instead WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471 WARNING:root:â•── 'batch_scan_layers' is deprecated. Use 'scan' instead WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
SANITY CHECKING¶
- inspecting andata and ldata objects (cell and gene counts)
- checking for duplicates
In [4]:
print("=== Seurat-derived AnnData (adata) ===")
print("Cells (obs):", adata.n_obs)
print("Genes (var):", adata.n_vars)
print("\nFirst 10 cell names:", adata.obs.index[:10].tolist())
print("\nFirst 10 gene names:", adata.var.index[:10].tolist())
print("\n\n=== Loom RNA velocity AnnData (ldata) ===")
print("Cells (obs):", ldata.n_obs)
print("Genes (var):", ldata.n_vars)
print("\nFirst 10 cell names:", ldata.obs.index[:10].tolist())
print("\nFirst 10 gene names:", ldata.var.index[:10].tolist())
print("\n\n=== Layer shapes in ldata ===")
for layer in ["spliced", "unspliced", "ambiguous"]:
if layer in ldata.layers:
print(f"{layer}: {ldata.layers[layer].shape}")
# check for duplicates in adata and ladata
print("\n\n=== Checking for dupicates ===")
print("Total cells in adata:", len(adata.obs.index))
print("Unique cells in adata:", len(adata.obs.index.unique()))
print("Duplicate barcodes in adata:", len(adata.obs.index) - len(adata.obs.index.unique()))
print("\nTotal cells in ldata:", len(ldata.obs.index))
print("Unique cells in ldata:", len(ldata.obs.index.unique()))
print("Duplicate barcodes in ldata:", len(ldata.obs.index) - len(ldata.obs.index.unique()))
# Show some duplicates if they exist
from collections import Counter
adata_counts = Counter(adata.obs.index)
adata_duplicates = {bc: count for bc, count in adata_counts.items() if count > 1}
print(f"\nNumber of duplicated barcodes: {len(adata_duplicates)}")
if adata_duplicates:
print("Examples:", list(adata_duplicates.items())[:5])
=== Seurat-derived AnnData (adata) ===
Cells (obs): 35317
Genes (var): 30481
First 10 cell names: ['AAACCCAAGAACAGGA', 'AAACCCAAGTCTCTGA', 'AAACGAAAGACTACGG', 'AAACGAAAGATTCGCT', 'AAACGAAAGCTCACTA', 'AAACGAACAGCTGTAT', 'AAACGAACATCCTTGC', 'AAACGAAGTACTGACT', 'AAACGAAGTGTATCCA', 'AAACGAAGTTGCTCGG']
First 10 gene names: ['Xkr4', 'Gm19938', 'Sox17', 'Mrpl15', 'Lypla1', 'Tcea1', 'Rgs20', 'Atp6v1h', 'Npbwr1', '4732440D04Rik']
=== Loom RNA velocity AnnData (ldata) ===
Cells (obs): 45487
Genes (var): 33696
First 10 cell names: ['AAAGGGCAGTCATACC', 'AAAGGTATCGGAAGGT', 'AAATGGACACTCAAGT', 'AAAGAACCAGTTGTTG', 'AAACGAACATCCTTGC', 'AAAGGATTCCAATCTT', 'AAATGGAAGTGGAAAG', 'AAAGTCCAGAACGCGT', 'AAAGTGAGTCACGTGC', 'AAAGGGCGTTGTCTAG']
First 10 gene names: ['ENSMUSG00000079800', 'ENSMUSG00000095092', 'ENSMUSG00000079794', 'ENSMUSG00000079192', 'ENSMUSG00000094799', 'ENSMUSG00000095250', 'ENSMUSG00000095787', 'ENSMUSG00000095672', 'ENSMUSG00000094514', 'ENSMUSG00000096100']
=== Layer shapes in ldata ===
spliced: (45487, 33696)
unspliced: (45487, 33696)
ambiguous: (45487, 33696)
=== Checking for dupicates ===
Total cells in adata: 35317
Unique cells in adata: 35173
Duplicate barcodes in adata: 144
Total cells in ldata: 45487
Unique cells in ldata: 45252
Duplicate barcodes in ldata: 235
Number of duplicated barcodes: 143
Examples: [('AAACGAAAGATTCGCT', 2), ('AAACGAATCTCAACCC', 2), ('AACAAGAGTACCTAGT', 2), ('AAGCATCTCGTCAGAT', 2), ('AATGGCTTCGCTAATG', 2)]
In [5]:
# Remove duplicates from both datasets (keep first occurrence)
print("\n=== Removing duplicates ===")
adata = adata[~adata.obs.index.duplicated(keep='first'), :]
ldata = ldata[~ldata.obs.index.duplicated(keep='first'), :]
print(f"adata after dedup: {adata.shape}")
print(f"ldata after dedup: {ldata.shape}")
# Find common barcodes
common_barcodes = set(adata.obs.index).intersection(set(ldata.obs.index))
print(f"\n=== Common cells ===")
print(f"Cells in common: {len(common_barcodes)}")
# Subset both datasets to only common cells
# Convert to list and sort for reproducibility
common_barcodes = sorted(list(common_barcodes))
adata = adata[common_barcodes, :]
ldata = ldata[common_barcodes, :]
print(f"\n=== Final datasets ===")
print(f"Final adata shape: {adata.shape}")
print(f"Final ldata shape: {ldata.shape}")
print(f"Indices match: {all(adata.obs.index == ldata.obs.index)}")
=== Removing duplicates === adata after dedup: (35173, 30481) ldata after dedup: (45252, 33696) === Common cells === Cells in common: 34946 === Final datasets === Final adata shape: (34946, 30481) Final ldata shape: (34946, 33696) Indices match: True
In [6]:
# converting the loom's ENSEMBL ID's to match
mg = mygene.MyGeneInfo()
gene_index = ldata.var.index.to_series()
# only grab the genes that have ENSEMBL IDs
is_ensembl = gene_index.str.startswith("ENSMUSG")
print("Total genes:", gene_index.shape[0])
print("ENSEMBL-like genes:", is_ensembl.sum())
print("Already-symbol-like genes:", (~is_ensembl).sum(), '\n')
# only query the ENSMUSG IDs
ens_ids = gene_index[is_ensembl].unique().tolist()
results = mg.querymany(
ens_ids,
scopes="ensemblgene", # or "ensembl.gene" depending on mygene version, but this usually works
fields="symbol",
species="mouse",
as_dataframe=False
)
# Build mapping dict ENSMUSG -> symbol
ens_to_symbol = {r["query"]: r.get("symbol", None) for r in results}
# QC on mapping
total_ens = len(ens_ids)
mapped_ens = sum(v is not None for v in ens_to_symbol.values())
print("Total ENSMUSG IDs:", total_ens)
print("Mapped ENSMUSG → symbol:", mapped_ens)
print("Unmapped ENSMUSG:", total_ens - mapped_ens)
# 4) Create a 'symbol' column:
# default: keep existing name
ldata.var["symbol"] = gene_index.copy()
# replace ENSMUSG entries with their symbol
for g in gene_index[is_ensembl]:
sym = ens_to_symbol.get(g, None)
if sym is not None:
ldata.var.at[g, "symbol"] = sym
ldata.var.index = ldata.var["symbol"]
gene_index = ldata.var.index.to_series()
is_ensembl = gene_index.str.startswith("ENSMUSG")
print("Total ENSMUSG IDs after mapping: ", is_ensembl.sum())
WARNING:biothings.client:Input sequence provided is already in string format. No operation performed WARNING:biothings.client:Input sequence provided is already in string format. No operation performed INFO:biothings.client:querying 1-248 ...
Total genes: 33696 ENSEMBL-like genes: 248 Already-symbol-like genes: 33448
INFO:biothings.client:Finished. WARNING:biothings.client:13 input query terms found no hit: ['ENSMUSG00000095742', 'ENSMUSG00000095728', 'ENSMUSG00000095076', 'ENSMUSG00000121317', 'ENSMUSG000 INFO:biothings.client:Pass "returnall=True" to return complete lists of duplicate or missing query terms.
Total ENSMUSG IDs: 248 Mapped ENSMUSG → symbol: 203 Unmapped ENSMUSG: 45 Total ENSMUSG IDs after mapping: 45
In [7]:
# Intersect with Seurat genes
ldata.var_names_make_unique() # This handles any duplicate gene symbol
print("Total number of var names: ", len(adata.var_names))
# Now find common genes between the two datasets
common_genes = adata.var.index.intersection(ldata.var.index)
print("Overlapping genes after symbol mapping:", len(common_genes))
# Subset both datasets to common genes
adata_subset = adata[:, common_genes].copy()
ldata_subset = ldata[:, common_genes].copy()
print(f"adata shape: {adata_subset.shape}")
print(f"ldata shape: {ldata_subset.shape}")
Total number of var names: 30481 Overlapping genes after symbol mapping: 29365 adata shape: (34946, 29365) ldata shape: (34946, 29365)
In [8]:
# Sanity Checks
# Verify cell barcodes match
print("Cells match:", (adata_subset.obs.index == ldata_subset.obs.index).all())
# If they don't match, reorder ldata_subset to match adata_subset:
ldata_subset = ldata_subset[adata_subset.obs.index, :].copy()
# Double-check genes are in same order
print("Genes match:", (adata_subset.var.index == ldata_subset.var.index).all())
Cells match: True Genes match: True
Integrating Loom and OWHA object¶
In [9]:
# Add velocity layers to adata_subset
adata_subset.layers["spliced"] = ldata_subset.layers["spliced"].copy()
adata_subset.layers["unspliced"] = ldata_subset.layers["unspliced"].copy()
adata_subset.layers["ambiguous"] = ldata_subset.layers["ambiguous"].copy()
# Verify they were added
print("Layers in adata_subset:", list(adata_subset.layers.keys()))
print("Spliced shape:", adata_subset.layers["spliced"].shape)
print("Unspliced shape:", adata_subset.layers["unspliced"].shape)
Layers in adata_subset: ['spliced', 'unspliced', 'ambiguous'] Spliced shape: (34946, 29365) Unspliced shape: (34946, 29365)
In [10]:
adata_subset.obs
Out[10]:
| orig.ident | nCount_RNA | nFeature_RNA | timepoint | nCount_ADT | nFeature_ADT | percent_mito | percent_ribo | timepoint_modality | nCount_SCT | ... | gptcelltype | sctype_skinDB | singleR | celltype | celltype_fine | metaclusters | StressScore1 | TF percentage | nCount_RNA_v4 | nFeature_RNA_v4 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AAACCCAAGAACAGGA | UW_CITEseq_1 | 4246.0 | 1723 | Unwounded | 399.0 | 78 | 8.431465 | 6.947715 | Unwounded_CITEseq | 8358.0 | ... | Fibroblasts | Cycling cells | Cardiomyocytes | Pericytes | Pericyte II | Pericytes | 0.975801 | 7.348092 | 4246.0 | 1723 |
| AAACCCAAGATACAGT | D30PW_CITEseq_1 | 5424.0 | 2026 | Wounded_D30PW | 239.0 | 69 | 5.530973 | 6.526549 | Wounded_D30PW_CITEseq | 7201.0 | ... | Keratinocytes | Cycling cells | Neurons | HF Keratinocytes | IRS II | HF Keratinocytes | 0.010937 | 8.001475 | 5424.0 | 2026 |
| AAACCCAAGCAATAGT | D15PW_CITEseq_2 | 5251.0 | 1547 | Wounded_D15PW | 1507.0 | 98 | 1.256903 | 26.128357 | Wounded_D15PW_CITEseq | 6036.0 | ... | Keratinocytes | Unknown | T cells | Dendritic cells | cDC2 | Immune cells | -0.038145 | 3.446962 | 5251.0 | 1547 |
| AAACCCAAGCGCCTAC | D15PW_CITEseq_2 | 6564.0 | 2217 | Wounded_D15PW | 1846.0 | 99 | 1.416819 | 12.568556 | Wounded_D15PW_CITEseq | 6529.0 | ... | Keratinocytes | Schwann cells | Microglia | Macrophages | Neutrophils II | Immune cells | 0.267384 | 6.230957 | 6564.0 | 2217 |
| AAACCCAAGCTAGTTC | D15PW_CITEseq_1 | 6762.0 | 2138 | Wounded_D15PW | 1862.0 | 100 | 1.286602 | 12.407572 | Wounded_D15PW_CITEseq | 6697.0 | ... | Fibroblasts | Unknown | Microglia | Macrophages | Macrophages III | Immune cells | 0.501483 | 4.702751 | 6762.0 | 2138 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| TTTGTTGTCTCAGTCC | D30PW_CITEseq_1 | 16213.0 | 3284 | Wounded_D30PW | 260.0 | 66 | 1.443286 | 32.757664 | Wounded_D30PW_CITEseq | 8354.0 | ... | Keratinocytes | Suprabasal Keratinocytes | B cells | IFE Keratinocytes | Spinous I | IFE Keratinocytes | 0.377910 | 3.904274 | 16213.0 | 3284 |
| TTTGTTGTCTCTGCTG | D30PW_CITEseq_2 | 15672.0 | 4255 | Wounded_D30PW | 628.0 | 85 | 3.088310 | 24.183257 | Wounded_D30PW_CITEseq | 5257.0 | ... | Schwann cells | Cycling cells | Erythrocytes | Proliferating Keratinocytes | Ker.Cycling II | HF Keratinocytes | 0.220671 | 6.202144 | 15672.0 | 4255 |
| TTTGTTGTCTGCGAGC | D15PW_CITEseq_2 | 14728.0 | 3067 | Wounded_D15PW | 1545.0 | 101 | 2.783813 | 27.206681 | Wounded_D15PW_CITEseq | 6825.0 | ... | Unknown | Suprabasal Keratinocytes | Oligodendrocytes | IFE Keratinocytes | Spinous III | IFE Keratinocytes | 0.167667 | 3.102933 | 14728.0 | 3067 |
| TTTGTTGTCTGGAAGG | D15PW_CITEseq_1 | 5141.0 | 1741 | Wounded_D15PW | 1740.0 | 97 | 1.225443 | 0.641898 | Wounded_D15PW_CITEseq | 5966.0 | ... | Keratinocytes | Fibroblasts | Astrocytes | Fibroblasts | Nfkb+ Fibroblasts | Fibroblasts | 0.005348 | 9.258899 | 5141.0 | 1741 |
| TTTGTTGTCTGGTGGC | D15PW_CITEseq_1 | 3119.0 | 1472 | Wounded_D15PW | 1602.0 | 98 | 1.090093 | 9.009298 | Wounded_D15PW_CITEseq | 6053.0 | ... | Keratinocytes | Macrophages | Microglia | Macrophages | Macrophages III | Immune cells | 0.523043 | 6.572619 | 3119.0 | 1472 |
34946 rows × 28 columns
In [11]:
adata_subset.layers.keys()
Out[11]:
KeysView(Layers with keys: spliced, unspliced, ambiguous)
Starting RNA Velocity!¶
Now that we have combined the .loom file with our exported Seurat object (now AnnData object) we can explore with RNA Velocity
In [12]:
adata_subset.obsm.keys()
Out[12]:
KeysView(AxisArrays with keys: X_cca, X_harmony, X_pca, X_rpca, X_umap.cca, X_umap.harmony, X_umap.pca, X_umap.rpca)
In [13]:
# plot umap to check
adata_subset.obsm["X_umap"] = adata_subset.obsm["X_umap.rpca"].copy()
sc.pl.umap(adata_subset, color="celltype", frameon=False,
legend_loc='on data', title='', save='_celltypes_rpca.pdf')
WARNING: saving figure to file figures/umap_celltypes_rpca.pdf
In [14]:
scv.pl.proportions(adata_subset, groupby='celltype')
In [15]:
adata_subset.obsm["X_pca"].shape
Out[15]:
(34946, 50)
In [16]:
# pre-process
scv.pp.filter_and_normalize(adata_subset, min_shared_counts=20)
sc.pp.highly_variable_genes(adata_subset, n_top_genes=2000)
# subset to HVGs
adata_hvg = adata_subset[:, adata_subset.var['highly_variable']].copy()
# recompute neighbors on HVG PCA
scv.pp.moments(adata_hvg, n_pcs=30, n_neighbors=30)
Filtered out 17472 genes that are detected 20 counts (shared). WARNING: Did not normalize X as it looks processed already. To enforce normalization, set `enforce=True`. Normalized count data: spliced, unspliced.
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/preprocessing/utils.py:705: DeprecationWarning: `log1p` is deprecated since scVelo v0.3.0 and will be removed in a future version. Please use `log1p` from `scanpy.pp` instead. log1p(adata)
Logarithmized X.
/var/folders/hq/r4mfshzj3dq22fq4382_72qw0000gp/T/ipykernel_20518/1409331441.py:9: DeprecationWarning: Automatic neighbor calculation is deprecated since scvelo==0.4.0 and will be removed in a future version of scVelo. Please compute neighbors first with Scanpy. scv.pp.moments(adata_hvg, n_pcs=30, n_neighbors=30) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/preprocessing/moments.py:71: DeprecationWarning: `neighbors` is deprecated since scvelo==0.4.0 and will be removed in a future version of scVelo. Please compute neighbors with Scanpy. neighbors(
computing neighbors
finished (0:00:13) --> added
'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
finished (0:00:02) --> added
'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
In [17]:
# compute velocity ( this step will take a while )
try:
scv.tl.recover_dynamics(adata_hvg, n_top_genes=500)
scv.tl.velocity(adata_hvg, mode='dynamical')
scv.tl.velocity_graph(adata_hvg)
except Exception as e:
print("Error while fitting dynamics:", e)
print("Current gene index:", adata_hvg.var_names[adata_hvg.var['fit_alpha'].isna()].tolist()[:10])
recovering dynamics (using 1/16 cores)
WARNING: Unable to create progress bar. Consider installing `tqdm` as `pip install tqdm` and `ipywidgets` as `pip install ipywidgets`,
or disable the progress bar using `show_progress_bar=False`.
finished (0:11:37) --> added
'fit_pars', fitted parameters for splicing dynamics (adata.var)
computing velocities
finished (0:00:04) --> added
'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/16 cores)
finished (0:00:11) --> added
'velocity_graph', sparse matrix with cosine correlations (adata.uns)
In [18]:
scv.pl.velocity_embedding_grid(
adata_hvg,
basis='X_umap',
color='celltype',
dpi=150
)
computing velocity embedding
finished (0:00:01) --> added
'velocity_umap', embedded velocity vectors (adata.obsm)
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
In [19]:
scv.pl.velocity_embedding(adata_hvg,
arrow_length=3,
arrow_size=2,
color='celltype',
dpi=120)
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
In [20]:
scv.tl.rank_velocity_genes(adata_hvg, groupby='celltype')
df = scv.get_df(adata_hvg.uns['rank_velocity_genes']['names'])
df.head()
ranking velocity genes
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/tools/utils.py:463: DeprecationWarning: Please import `rankdata` from the `scipy.stats` namespace; the `scipy.stats.stats` namespace is deprecated and will be removed in SciPy 2.0.0. from scipy.stats.stats import rankdata
finished (0:00:06) --> added
'rank_velocity_genes', sorted scores by group ids (adata.uns)
'spearmans_score', spearmans correlation scores (adata.var)
/var/folders/hq/r4mfshzj3dq22fq4382_72qw0000gp/T/ipykernel_20518/2477482753.py:2: DeprecationWarning: `get_df` is deprecated since scvelo==0.4.0 and will be removed in a future version of scVelo. Please `AnnData::get_df` or Scanpy's `scanpy.get.obs_df` or `scanpy.get.var_df`. df = scv.get_df(adata_hvg.uns['rank_velocity_genes']['names'])
Out[20]:
| Neutrophils | Dendritic cells | Fibroblasts | Macrophages | IFE Keratinocytes | T cells | Endothelial cells | Proliferating Keratinocytes | HF Keratinocytes | Muscle cells | Pericytes | Sebocytes | Melanocytes | Langerhans cells | Proliferating Fibroblasts | Schwann cells | Mast cells | RBCs | Proliferating immune cells | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | Laptm5 | Basp1 | Ugdh | Basp1 | Anxa1 | Lcp2 | Mef2c | Itga6 | Hspg2 | Actb | Lamc1 | Itga6 | Zbtb20 | Pkib | Fstl1 | Nid1 | Lgals1 | Csf2ra | Basp1 |
| 1 | Crem | Plek | Dst | Itgb2 | Serpinb2 | Tm6sf1 | Nid1 | Lamc1 | Anxa8 | Mt1 | Zbtb20 | Anxa8 | Rgl1 | Ctsc | Fgfr1 | Col5a2 | Pdpn | Actb | Crem |
| 2 | Tm6sf1 | Crem | Fgfr1 | Emilin2 | Plet1 | Sp100 | Rgl1 | Slc7a8 | Lamc1 | Vim | Serpine1 | Timp3 | Pcolce2 | Crem | Zbtb20 | Zbtb20 | Hexa | Mt1 | Itgb2 |
| 3 | Epsti1 | Itgb2 | Fstl1 | Slc15a3 | Fosb | Samhd1 | Ebf1 | Creb5 | Creb5 | Col6a2 | Col5a2 | Serpinb5 | Nid1 | Tnfaip2 | Col5a2 | Col6a2 | Man1a | Tnfaip2 | Cd300a |
| 4 | Soat1 | Lilrb4b | Dab2 | Lgals3 | Epha4 | Ms4a4c | Cd34 | Hspg2 | Itga6 | Pcolce2 | Fstl1 | Gata3 | Rassf3 | Hexa | Axl | Lama2 | Ctsc | Ly86 | Plek |
In [21]:
for cluster in ['IFE Keratinocytes', 'Fibroblasts', 'Proliferating immune cells', 'Proliferating Fibroblasts']:
scv.pl.scatter(adata_hvg, df[cluster][:5], ylabel=cluster, frameon=False, color='celltype')
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
In [23]:
scv.pl.scatter(adata_hvg, color='celltype', basis=adata_hvg.uns["rank_velocity_genes"]["names"]["IFE Keratinocytes"][:3])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
In [24]:
scv.pl.velocity(adata_hvg, ['Epb41l2'], color='celltype')
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
In [25]:
scv.pl.velocity(adata_hvg, ['Mki67'], color='celltype') # Proliferating Keratinocytes
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
In [26]:
scv.tl.latent_time(adata_hvg)
scv.pl.scatter(adata_hvg, color='latent_time', color_map='gnuplot', size=80)
computing terminal states
identified 9 regions of root cells and 2 regions of end points .
finished (0:00:10) --> added
'root_cells', root cells of Markov diffusion process (adata.obs)
'end_points', end points of Markov diffusion process (adata.obs)
computing latent time using root_cells as prior
finished (0:00:03) --> added
'latent_time', shared time (adata.obs)
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
In [27]:
top_genes = adata_hvg.var['fit_likelihood'].sort_values(ascending=False).index[:300]
scv.pl.heatmap(adata_hvg, var_names=top_genes, sortby='latent_time', col_color='metaclusters', n_convolve=100)
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
In [33]:
scv.pl.scatter(adata_hvg, color='latent_time', color_map='viridis')
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
In [28]:
top_genes
Out[28]:
Index(['Dmkn', 'Cytip', 'Perp', 'Hmox1', 'Zeb2', 'Fstl1', 'F13a1', 'Serpinb5',
'Ifi205', 'Oasl1',
...
'Nlrp3', 'Slc7a8', 'Slfn2', 'Actb', 'Igf1', 'Emilin2', 'Tnfaip6',
'Kitl', 'Col6a2', 'Fcgrt'],
dtype='object', length=300)
In [29]:
scv.pl.velocity(adata_hvg, ['Cfp'], color='celltype')
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
In [30]:
top_genes = adata_hvg.var['fit_likelihood'].sort_values(ascending=False).index
scv.pl.scatter(adata_hvg, basis=top_genes[:15], ncols=5, frameon=False, color='celltype',)
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
In [31]:
var_names = ['Zbtb20', 'Celf2']
scv.pl.scatter(adata_hvg, var_names, frameon=False, color='celltype',)
scv.pl.scatter(adata_hvg, x='latent_time', y=var_names, frameon=False, color='celltype',)
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c]) /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])